NM_144573.4(NEXN):c.362C>A (p.Thr121Lys) AND multiple conditions

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Apr 28, 2022
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV003120068.5

Allele description [Variation Report for NM_144573.4(NEXN):c.362C>A (p.Thr121Lys)]

NM_144573.4(NEXN):c.362C>A (p.Thr121Lys)

Genes:

LOC126805765:BRD4-independent group 4 enhancer GRCh37_chr1:78383688-78384887 [Gene]
NEXN:nexilin F-actin binding protein [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

1p31.1

Genomic location:

Preferred name:

NM_144573.4(NEXN):c.362C>A (p.Thr121Lys)

HGVS:

NC_000001.11:g.77918188C>A
NG_016625.1:g.34674C>A
NG_082089.1:g.286C>A
NM_001172309.2:c.170C>A
NM_144573.4:c.362C>AMANE SELECT
NP_001165780.1:p.Thr57Lys
NP_653174.3:p.Thr121Lys
NP_653174.3:p.Thr121Lys
LRG_442t1:c.362C>A
LRG_442:g.34674C>A
LRG_442p1:p.Thr121Lys
NC_000001.10:g.78383873C>A
NM_144573.3:c.362C>A

Protein change:

T121K

Molecular consequence:

NM_001172309.2:c.170C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_144573.4:c.362C>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Dilated cardiomyopathy 1CC (CMD1CC)
Identifiers:: MONDO: MONDO:0013147; MedGen: C2751084; Orphanet: 154; OMIM: 613122

Name:: Hypertrophic cardiomyopathy 20
Synonyms:: Familial hypertrophic cardiomyopathy 20
Identifiers:: MONDO: MONDO:0013477; MedGen: C3151267; OMIM: 613876

Recent activity

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zt08d07.r1 NCI_CGAP_GCB1 Homo sapiens cDNA clone IMAGE:712525 5', mRNA sequence
zt08d07.r1 NCI_CGAP_GCB1 Homo sapiens cDNA clone IMAGE:712525 5', mRNA sequence
gi|1921705|gnl|dbEST|921085|gb|AA27 1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003796737	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Apr 28, 2022)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003796737

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Apr 28, 2022)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV003796737.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

Description

This sequence change replaces threonine, which is neutral and polar, with lysine, which is basic and polar, at codon 121 of the NEXN protein (p.Thr121Lys). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with NEXN-related conditions. Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be tolerated. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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